Genetic Diversity and Genome-Wide Association Study of Major Ear Quantitative Traits Using High-Density SNPs in Maize

Kernel and ear traits are key components of grain yield in maize (Zea mays L.). Investigation of these traits would help to develop high-yield varieties in maize. Genome-wide association study (GWAS) uses the linkage disequilibrium (LD) in the whole genome to determine the genes affecting certain phenotype. In this study, five ear traits (kernel length and width, ear length and diameter, cob diameter) were investigated across multi-environments for 2 years. Combining with the genotype obtained from Maize SNP50 chip, genetic diversity and association mapping in a set of 292 inbred lines were performed. Results showed that maize lines were clustered into seven subgroups and a total of 20 SNPs were found to be associated with ear traits significantly (P < 3.95E-05). The candidate genes identified by GWAS mainly encoded ubiquitin-activation enzymes (GRMZM2G015287), carotenoid cleavage dioxygenase (GRMZM2G446858), MYB-CC type transfactor, and phosphate starvation response protein 3, and they were associated with kernel length (KL) and ear diameter (ED), respectively. Moreover, two novel genes corresponding to RNA processing and fructose metabolism were found. Further, the SNPs detected by GWAS were confirmed by meta-QTL analysis. These genes and SNPs identified in the study would offer essential information for yield-related genes clone and breeding program in maize.